Holdemania filiformis (DSM 12042, ATCC 51649, CCUG 39501)

Name: Holdemania filiformis (DSM 12042, ATCC 51649, CCUG 39501)
Creator: BacDive
License: http://creativecommons.org/licenses/by/4.0/

BacDive ID 5373

Type strain

Culture col. no. DSM 12042 ATCC 51649 CCUG 39501 VPI J1-31B-1

NCBI tax ID(s) 545696 61171

Special Collections DSMZ CCUG

Links

Holdemania filiformis DSM 12042 is an anaerobe, mesophilic prokaryote that was isolated from human feces.

anaerobe mesophilic genome sequence 16S sequence

Name and taxonomic classification

SI-ID 45309

ATCC 51649,CCUG 39501,DSM 12042

@ref 20215

Last LPSN update 2025-12-16 09:48:03

Domain Bacillati

Phylum Bacillota

Class Erysipelotrichia

Order Erysipelotrichales

Family Erysipelotrichaceae

Genus Holdemania

Species Holdemania filiformis

Full scientific name Holdemania filiformis Willems et al. 1997

Morphology

Culture and growth conditions

Culture medium

@ref	Name	Growth	Medium link	Composition
4586	PYG MEDIUM (MODIFIED) (DSMZ Medium 104)		Medium recipe at MediaDive	Name: PYG MEDIUM (modified) (DSMZ Medium 104) Composition: Yeast extract 10.0 g/l Peptone 5.0 g/l Trypticase peptone 5.0 g/l Beef extract 5.0 g/l Glucose 5.0 g/l L-Cysteine HCl x H2O 0.5 g/l NaHCO3 0.4 g/l NaCl 0.08 g/l K2HPO4 0.04 g/l KH2PO4 0.04 g/l MgSO4 x 7 H2O 0.02 g/l CaCl2 x 2 H2O 0.01 g/l Hemin 0.005 g/l Ethanol 0.0038 g/l Resazurin 0.001 g/l Tween 80 Vitamin K1 NaOH Distilled water

Culture temp

@ref	Growth	Type	Temperature (°C)	Range
4586	positive	growth	37	mesophilic

Physiology and metabolism

Oxygen tolerance

@ref	Oxygen tolerance	Confidence
4586	anaerobe
125439	microaerophile	92.5

Murein

@ref	Murein short key	Type
4586	B13	B1delta {L-Ser} [L-Ala] D-Glu-L-Asp-L-Lys

Metabolite utilization

@ref	Chebi-ID	Metabolite	Utilization activity	Kind of utilization tested
68380	29016 ChEBI	arginine	-	hydrolysis	from API rID32A
68380	16024 ChEBI	D-mannose	-	fermentation	from API rID32A
68380	29985 ChEBI	L-glutamate	-	degradation	from API rID32A
68380	17632 ChEBI	nitrate	-	reduction	from API rID32A
68380	16634 ChEBI	raffinose	-	fermentation	from API rID32A
68380	27897 ChEBI	tryptophan	-	energy source	from API rID32A
68380	16199 ChEBI	urea	-	hydrolysis	from API rID32A

Metabolite production

@ref	Chebi-ID	Metabolite	Production
68380	35581 ChEBI	indole		from API rID32A

Metabolite tests

@ref	Chebi-ID	Metabolite	Indole test
68380	35581 ChEBI	indole	-	from API rID32A

Enzymes

@ref	Value	Activity	Ec
68380	alanine arylamidase	-	3.4.11.2	from API rID32A
68380	alkaline phosphatase	-	3.1.3.1	from API rID32A
68380	alpha-arabinosidase	-	3.2.1.55	from API rID32A
68380	alpha-fucosidase	+	3.2.1.51	from API rID32A
68380	alpha-galactosidase	-	3.2.1.22	from API rID32A
68380	arginine dihydrolase	-	3.5.3.6	from API rID32A
68380	beta-galactosidase	+	3.2.1.23	from API rID32A
68380	beta-Galactosidase 6-phosphate	-		from API rID32A
68380	beta-glucosidase	-	3.2.1.21	from API rID32A
68380	beta-glucuronidase	-	3.2.1.31	from API rID32A
68380	glutamate decarboxylase	-	4.1.1.15	from API rID32A
68380	glutamyl-glutamate arylamidase	+		from API rID32A
68380	glycin arylamidase	-		from API rID32A
68380	histidine arylamidase	-		from API rID32A
68380	L-arginine arylamidase	-		from API rID32A
68380	leucine arylamidase	-	3.4.11.1	from API rID32A
68380	leucyl glycin arylamidase	-	3.4.11.1	from API rID32A
68380	N-acetyl-beta-glucosaminidase	-	3.2.1.52	from API rID32A
68380	phenylalanine arylamidase	-		from API rID32A
68380	proline-arylamidase	-	3.4.11.5	from API rID32A
68380	pyrrolidonyl arylamidase	+	3.4.19.3	from API rID32A
68380	serine arylamidase	-		from API rID32A
68380	tryptophan deaminase	-	4.1.99.1	from API rID32A
68380	tyrosine arylamidase	+		from API rID32A
68380	urease	-	3.5.1.5	from API rID32A

Pathway annotation

Computationally determined by

@ref	pathway	enzyme coverage	annotated reactions
66794	cellulose degradation	100	5 of 5
66794	threonine metabolism	100	10 of 10
66794	L-lactaldehyde degradation	100	3 of 3
66794	methylglyoxal degradation	100	5 of 5
66794	aspartate and asparagine metabolism	100	9 of 9
66794	coenzyme A metabolism	100	4 of 4
66794	teichoic acid biosynthesis	100	1 of 1
66794	CDP-diacylglycerol biosynthesis	100	2 of 2
66794	UDP-GlcNAc biosynthesis	100	3 of 3
66794	folate polyglutamylation	100	1 of 1
66794	peptidoglycan biosynthesis	93.33	14 of 15
66794	chorismate metabolism	88.89	8 of 9
66794	NAD metabolism	83.33	15 of 18
66794	Entner Doudoroff pathway	80	8 of 10
66794	glycogen metabolism	80	4 of 5
66794	glycine betaine biosynthesis	80	4 of 5
66794	valine metabolism	77.78	7 of 9
66794	d-mannose degradation	77.78	7 of 9
66794	serine metabolism	77.78	7 of 9
66794	palmitate biosynthesis	77.27	17 of 22
66794	phenylalanine metabolism	76.92	10 of 13
66794	CMP-KDO biosynthesis	75	3 of 4
66794	glycogen biosynthesis	75	3 of 4
66794	C4 and CAM-carbon fixation	75	6 of 8
66794	ppGpp biosynthesis	75	3 of 4
66794	acetate fermentation	75	3 of 4
66794	purine metabolism	73.4	69 of 94
66794	pyrimidine metabolism	73.33	33 of 45
66794	photosynthesis	71.43	10 of 14
66794	glycolysis	70.59	12 of 17
66794	starch degradation	70	7 of 10
66794	myo-inositol biosynthesis	70	7 of 10
66794	octane oxidation	66.67	2 of 3
66794	methane metabolism	66.67	2 of 3
66794	formaldehyde oxidation	66.67	2 of 3
66794	acetoin degradation	66.67	2 of 3
66794	glycolate and glyoxylate degradation	66.67	4 of 6
66794	gluconeogenesis	62.5	5 of 8
66794	degradation of hexoses	61.11	11 of 18
66794	factor 420 biosynthesis	60	3 of 5
66794	metabolism of amino sugars and derivatives	60	3 of 5
66794	hydrogen production	60	3 of 5
66794	oxidative phosphorylation	59.34	54 of 91
66794	degradation of aromatic, nitrogen containing compounds	58.33	7 of 12
66794	glutamate and glutamine metabolism	57.14	16 of 28
66794	propanol degradation	57.14	4 of 7
66794	degradation of sugar acids	56	14 of 25
66794	metabolism of disaccharids	54.55	6 of 11
66794	pentose phosphate pathway	54.55	6 of 11
66794	flavin biosynthesis	53.33	8 of 15
66794	non-pathway related	52.63	20 of 38
66794	alanine metabolism	51.72	15 of 29
66794	cis-vaccenate biosynthesis	50	1 of 2
66794	kanosamine biosynthesis II	50	1 of 2
66794	ribulose monophosphate pathway	50	1 of 2
66794	methionine metabolism	50	13 of 26
66794	mannosylglycerate biosynthesis	50	1 of 2
66794	suberin monomers biosynthesis	50	1 of 2
66794	ethanol fermentation	50	1 of 2
66794	citric acid cycle	50	7 of 14
66794	phenylmercury acetate degradation	50	1 of 2
66794	quinate degradation	50	1 of 2
66794	sphingosine metabolism	50	3 of 6
66794	butanoate fermentation	50	2 of 4
66794	adipate degradation	50	1 of 2
66794	glutathione metabolism	50	7 of 14
66794	degradation of pentoses	46.43	13 of 28
66794	vitamin B1 metabolism	46.15	6 of 13
66794	vitamin B6 metabolism	45.45	5 of 11
66794	ascorbate metabolism	45.45	10 of 22
66794	molybdenum cofactor biosynthesis	44.44	4 of 9
66794	ubiquinone biosynthesis	42.86	3 of 7
66794	cardiolipin biosynthesis	42.86	3 of 7
66794	tyrosine metabolism	42.86	6 of 14
66794	isoprenoid biosynthesis	42.31	11 of 26
66794	lipoate biosynthesis	40	2 of 5
66794	glycine metabolism	40	4 of 10
66794	phenylpropanoid biosynthesis	38.46	5 of 13
66794	lysine metabolism	38.1	16 of 42
66794	isoleucine metabolism	37.5	3 of 8
66794	6-hydroxymethyl-dihydropterin diphosphate biosynthesis	37.5	3 of 8
66794	arginine metabolism	37.5	9 of 24
66794	ketogluconate metabolism	37.5	3 of 8
66794	tryptophan metabolism	36.84	14 of 38
66794	proline metabolism	36.36	4 of 11
66794	dolichyl-diphosphooligosaccharide biosynthesis	36.36	4 of 11
66794	d-xylose degradation	36.36	4 of 11
66794	tetrahydrofolate metabolism	35.71	5 of 14
66794	lipid metabolism	35.48	11 of 31
66794	polyamine pathway	34.78	8 of 23
66794	lipid A biosynthesis	33.33	3 of 9
66794	IAA biosynthesis	33.33	1 of 3
66794	acetyl CoA biosynthesis	33.33	1 of 3
66794	4-hydroxymandelate degradation	33.33	3 of 9
66794	selenocysteine biosynthesis	33.33	2 of 6
66794	sulfoquinovose degradation	33.33	1 of 3
66794	degradation of sugar alcohols	31.25	5 of 16
66794	histidine metabolism	31.03	9 of 29
66794	reductive acetyl coenzyme A pathway	28.57	2 of 7
66794	vitamin E metabolism	25	1 of 4
66794	dTDPLrhamnose biosynthesis	25	2 of 8
66794	toluene degradation	25	1 of 4
66794	carnitine metabolism	25	2 of 8
66794	cyclohexanol degradation	25	1 of 4
66794	biotin biosynthesis	25	1 of 4
66794	catecholamine biosynthesis	25	1 of 4
66794	lactate fermentation	25	1 of 4
66794	androgen and estrogen metabolism	25	4 of 16
66794	leucine metabolism	23.08	3 of 13
66794	urea cycle	23.08	3 of 13
66794	sulfate reduction	23.08	3 of 13
66794	CO2 fixation in Crenarchaeota	22.22	2 of 9
66794	cysteine metabolism	22.22	4 of 18
66794	nitrate assimilation	22.22	2 of 9
66794	allantoin degradation	22.22	2 of 9

API rID32A

@ref	URE	ADH (Arg)	alpha GAL	beta GAL	beta-Galactosidase 6-phosphatebeta GP	alpha GLU	beta GLU	alpha ARA	beta GUR	beta-N-Acetyl-beta-glucosaminidasebeta NAG	MNE	RAF	GDC	alpha FUC	Reduction of nitrateNIT	IND	PAL	L-arginine arylamidaseArgA	ProA	LGA	Phenylalanine arylamidasePheA	Leucine arylamidaseLeuA	PyrA	Tyrosine arylamidaseTyrA	Alanine arylamidaseAlaA	Glycin arylamidaseGlyA	Histidine arylamidaseHisA	Glutamyl-glutamate arylamidaseGGA	Serine arylamidaseSerA
4586	-	-	-	+	-	+/-	-	-	-	-	-	-	-	+	-	-	-	-	-	-	-	-	+	+	-	-	-	+	-

Isolation, sampling and environmental information

Isolation source categories

Cat1	Cat2	Cat3
#Host	#Human	-
#Host Body Product	#Gastrointestinal tract	#Feces (Stool)

Isolation

4586

Sample typehuman feces

Taxonmaps

69479

Global distribution of 16S sequence Y11466 (>99% sequence identity) for Holdemania filiformis from Microbeatlas

Aquatic Samples	486
Soil Samples	49
Animal Samples	34370
Plant Samples	14
Total Samples	34919

Interaction and safety

Risk assessment

@ref	Biosafety level	Biosafety level comment
4586	1	Risk group (German classification) According to TRBA 466

Sequence information

Genome sequences

@ref	Description	Assembly level	INSDC accession	BV-BRC accession	IMG accession	NCBI tax ID	Score
66792	ASM15799v1 assembly for Holdemania filiformis DSM 12042	scaffold	GCA_000157995	545696.5	643886103	545696	15.35

16S sequences

@ref	Description	Accession	Length	Database	NCBI tax ID
4586	H.filiformis 16S rRNA gene	Y11466	1391		61171

GC content

4586

GC-content (mol%)38

Genome-based predictions

Predictions

Predictions from Deep Learning for Genome Sequence Data. R package version 0.3.1 based on: Holdemania filiformis DSM 12042
NCBI: GCA_000157995

@ref	Trait	Model	Prediction	Confidence in %	In training data
125439	spore_formation	BacteriaNetⓘ	no	72.60	no
125439	motility	BacteriaNetⓘ	no	69.80	no
125439	gram_stain	BacteriaNetⓘ	variable	68.60	no
125439	oxygen_tolerance	BacteriaNetⓘ	microaerophile	92.50	no

Predictions from bacterial phenotypic traits through improved machine learning using high-quality, curated datasets based on: Holdemania filiformis DSM 12042 DSM 12042
NCBI: GCA_000157995.1

@ref	Trait	Model	Prediction	Confidence in %	In training data
125438	gram-positive	gram-positiveⓘ	yes	67.68	no
125438	anaerobic	anaerobicⓘ	yes	84.79	yes
125438	aerobic	aerobicⓘ	no	94.10	yes
125438	spore-forming	spore-formingⓘ	no	60.32	no
125438	thermophilic	thermophileⓘ	no	92.77	no
125438	flagellated	motile2+ⓘ	no	85.13	no

Literature

Topic	Title	Authors	Journal	DOI	Year
	Development of culture methods capable of culturing a wide range of predominant species of intestinal bacteria.	Hirano R, Nishita I, Nakai R, Bito A, Sasabe R, Kurihara S.	Front Cell Infect Microbiol	10.3389/fcimb.2023.1056866	2023
Metabolism	Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease.	Heinken A, Ravcheev DA, Baldini F, Heirendt L, Fleming RMT, Thiele I.	Microbiome	10.1186/s40168-019-0689-3	2019
Pathogenicity	Genetic manipulation of gut microbes enables single-gene interrogation in a complex microbiome.	Jin WB, Li TT, Huo D, Qu S, Li XV, Arifuzzaman M, Lima SF, Shi HQ, Wang A, Putzel GG, Longman RS, Artis D, Guo CJ.	Cell	10.1016/j.cell.2021.12.035	2022
	Tryptophan-Centric Bioinformatics Identifies New Lasso Peptide Modifications.	Harris LA, Saad H, Shelton KE, Zhu L, Guo X, Mitchell DA.	Biochemistry	10.1021/acs.biochem.4c00035	2024
Metabolism	Indoleacrylic Acid Produced by Commensal Peptostreptococcus Species Suppresses Inflammation.	Wlodarska M, Luo C, Kolde R, d'Hennezel E, Annand JW, Heim CE, Krastel P, Schmitt EK, Omar AS, Creasey EA, Garner AL, Mohammadi S, O'Connell DJ, Abubucker S, Arthur TD, Franzosa EA, Huttenhower C, Murphy LO, Haiser HJ, Vlamakis H, Porter JA, Xavier RJ.	Cell Host Microbe	10.1016/j.chom.2017.06.007	2017
Metabolism	Strain dropouts reveal interactions that govern the metabolic output of the gut microbiome.	Wang M, Osborn LJ, Jain S, Meng X, Weakley A, Yan J, Massey WJ, Varadharajan V, Horak A, Banerjee R, Allende DS, Chan ER, Hajjar AM, Wang Z, Dimas A, Zhao A, Nagashima K, Cheng AG, Higginbottom S, Hazen SL, Brown JM, Fischbach MA.	Cell	10.1016/j.cell.2023.05.037	2023
Genetics	Genomic analysis of the multi-host pathogen Erysipelothrix rhusiopathiae reveals extensive recombination as well as the existence of three generalist clades with wide geographic distribution.	Forde T, Biek R, Zadoks R, Workentine ML, De Buck J, Kutz S, Opriessnig T, Trewby H, van der Meer F, Orsel K.	BMC Genomics	10.1186/s12864-016-2643-0	2016
Genetics	Genome Sequencing of Mesonia algae K4-1 Reveals Its Adaptation to the Arctic Ocean.	Huan R, Huang J, Liu D, Wang M, Liu C, Zhang Y, Yi C, Xiao D, He H.	Front Microbiol	10.3389/fmicb.2019.02812	2019
	Functional Comparison of Bacteria from the Human Gut and Closely Related Non-Gut Bacteria Reveals the Importance of Conjugation and a Paucity of Motility and Chemotaxis Functions in the Gut Environment.	Dobrijevic D, Abraham AL, Jamet A, Maguin E, van de Guchte M.	PLoS One	10.1371/journal.pone.0159030	2016
	Autometa: automated extraction of microbial genomes from individual shotgun metagenomes.	Miller IJ, Rees ER, Ross J, Miller I, Baxa J, Lopera J, Kerby RL, Rey FE, Kwan JC.	Nucleic Acids Res	10.1093/nar/gkz148	2019
	In silico identification of bacteriocin gene clusters in the gastrointestinal tract, based on the Human Microbiome Project's reference genome database.	Walsh CJ, Guinane CM, Hill C, Ross RP, O'Toole PW, Cotter PD.	BMC Microbiol	10.1186/s12866-015-0515-4	2015
	Design, construction, and in vivo augmentation of a complex gut microbiome.	Cheng AG, Ho PY, Aranda-Diaz A, Jain S, Yu FB, Meng X, Wang M, Iakiviak M, Nagashima K, Zhao A, Murugkar P, Patil A, Atabakhsh K, Weakley A, Yan J, Brumbaugh AR, Higginbottom S, Dimas A, Shiver AL, Deutschbauer A, Neff N, Sonnenburg JL, Huang KC, Fischbach MA.	Cell	10.1016/j.cell.2022.08.003	2022
Metabolism	Alternative spermidine biosynthetic route is critical for growth of Campylobacter jejuni and is the dominant polyamine pathway in human gut microbiota.	Hanfrey CC, Pearson BM, Hazeldine S, Lee J, Gaskin DJ, Woster PM, Phillips MA, Michael AJ.	J Biol Chem	10.1074/jbc.m111.307835	2011
Enzymology	Solobacterium moorei bacteremia: identification, antimicrobial susceptibility, and clinical characteristics.	Pedersen RM, Holt HM, Justesen US.	J Clin Microbiol	10.1128/jcm.02525-10	2011
	Draft genome and description of Merdibacter massiliensis gen.nov., sp. nov., a new bacterium genus isolated from the human ileum.	Anani H, Abou Abdallah R, Chelkha N, Fontanini A, Ricaboni D, Mailhe M, Raoult D, Fournier PE.	Sci Rep	10.1038/s41598-019-44343-8	2019
Genetics	Non contiguous-finished genome sequence and description of Dielma fastidiosa gen. nov., sp. nov., a new member of the Family Erysipelotrichaceae.	Ramasamy D, Lagier JC, Nguyen TT, Raoult D, Fournier PE.	Stand Genomic Sci	10.4056/sigs.3567059	2013
Genetics	Non-contiguous finished genome sequence and description of Holdemania massiliensis sp. nov.	Mishra AK, Lagier JC, Pfleiderer A, Nguyen TT, Caputo A, Raoult D, Fournier PE.	Stand Genomic Sci	10.4056/sigs.4628316	2013
Phylogeny	Phenotypic and phylogenetic characterization of some Eubacterium-like isolates containing a novel type B wall murein from human feces: description of Holdemania filiformis gen. nov., sp. nov.	Willems A, Moore WE, Weiss N, Collins MD	Int J Syst Bacteriol	10.1099/00207713-47-4-1201	1997

References

#4586	Leibniz Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH ; Curators of the DSMZ; DSM 12042
#20215	Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.: List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. IJSEM ( DOI 10.1099/ijsem.0.004332 )
#66792	Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg Overmann: Automatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information) .
#66794	Antje Chang, Lisa Jeske, Sandra Ulbrich, Julia Hofmann, Julia Koblitz, Ida Schomburg, Meina Neumann-Schaal, Dieter Jahn, Dietmar Schomburg: BRENDA, the ELIXIR core data resource in 2021: new developments and updates. Nucleic Acids Res. 49: D498 - D508 2020 ( DOI 10.1093/nar/gkaa1025 , PubMed 33211880 )
#68380	Automatically annotated from API rID32A .
#69479	João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.: MicrobeAtlas 1.0 beta .
#125438	Julia Koblitz, Lorenz Christian Reimer, Rüdiger Pukall, Jörg Overmann: Predicting bacterial phenotypic traits through improved machine learning using high-quality, curated datasets. 2024 ( DOI 10.1101/2024.08.12.607695 )
#125439	Philipp Münch, René Mreches, Martin Binder, Hüseyin Anil Gündüz, Xiao-Yin To, Alice McHardy: deepG: Deep Learning for Genome Sequence Data. R package version 0.3.1 .
#126262	A. Lissin, I. Schober, J. F. Witte, H. Lüken, A. Podstawka, J. Koblitz, B. Bunk, P. Dawyndt, P. Vandamme, P. de Vos, J. Overmann, L. C. Reimer: StrainInfo—the central database for linked microbial strain identifiers. ( DOI 10.1093/database/baaf059 )

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Holdemania filiformis (DSM 12042, ATCC 51649, CCUG 39501)

Name and taxonomic classification

Morphology

Culture and growth conditions

Culture medium

Culture temp

Physiology and metabolism

Oxygen tolerance

Murein

Metabolite utilization

Metabolite production

Metabolite tests

Enzymes

Pathway annotation

API rID32A

Isolation, sampling and environmental information

Isolation source categories

Isolation

Taxonmaps

Interaction and safety

Risk assessment

Sequence information

Genome sequences

Genome browser: GCA_000157995

16S sequences

GC content

Genome-based predictions

Predictions

Literature

Literature

References

BacDive

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